Functional imaging and behavior in zebrafish

Research center

4 place Jussieu Tour 32
75005 Paris
Didier Chatenay


ED 564
Université Pierre et Marie Curie


UMR 8237


light-sheet microscopy
sensory-motor integration
circuit inference
Available to host a PhD student


Sensorimotor Computation underlying phototaxis in zebrafish. Sébastien Wolf, Alexis M. Dubreuil, Tommaso Bertoni, Urs Lucas Böhm, Volker Bormuth, Raphaël Candelier, Sophia Karpenko, David G. C. Hildebrand, Isaac H. Bianco, Rémi Monasson, Georges Debrégeas. Nature Communication, in press

Whole-brain functional imaging with two-photon light-sheet microscopy, S Wolf, W. Supatto, G. Debrégeas, P. Mahou, S. G Kruglik,J-M. Sintes, E. Beaurepaire, R. Candelier Nature Methods 12, 379–380 (2015)

An Amplitude Modulation/Demodulation Scheme for Whisker-Based Texture Perception, Y. Boubenec, L. N. Claverie, D. E. Shulz,G. Debrégeas, J. Neurosci. 34(33): 10832-10843 (2014)

Fast functional imaging of multiple brain regions in intact zebrafish larvae using Selective Plane Illumination Microscopy. T. Panier,S. Romano, R. Olive, T. Pietri, G. sumbre, R. Candelier, G. Debrégeas, Frontiers in Neural Circuits 7, 0065 (2013)

The role of fingerprints in the coding of tactile information probed with a biomimetic sensor, J. Scheibert, S. Leurent, A. Prevost et G. Debrégeas, Science 323 1503-1506 (2009). Reviewed in Science news, Science Update (radio), Science signaling, Nature news, Nature Research highlights, Nature Methods,Analytical Chemistry, Atten. Percept & Psych.

Signatures of granular microstructure in dense shear flows. D. Mueth, G. Debregeas, G. Karczmar, P. Eng, S. Nagel & H. Jaeger,Nature 406, 385-388 (2000)

Fields of research

Neurophysiology / systems neuroscience

Research Theme

The overall objective of the group is to unravel principles of neural computations underlying sensory-motor integration in the vertebrate brain. We use the zebrafish larva as it currently constitutes the only vertebrate system amenable to whole-brain recording with cellular resolution. Using one- or two-photon light-sheet microscopy, we are able to monitor the long-term activity of the quasi-entirety of the 100,000 neurons that comprise the animal brain, as it performs basic sensory-motor tasks. We combine these experimental developments with a strong theoretical and computational effort aiming at interpretating the large datasets produced by whole-brain imaging approaches. Dimensionality reduction and neural circuit inference methods are implemented in order to extract from these continuous recordings information regarding the neural circuits architecture. In the near future, we wish to combine brain-wide recordings with spatially-resolved optogenetics techniques in order to directly interrogate the neural circuits and thus test network models.

We currently focus on 3 different topics :

Phototaxis: this behavior drives the animal to swim towards a light source. We study how the closed-loop coupling between visual stimuli, eyes saccades and tail beats allows the animal to perform such a task. We seek to further identify the neural integrator circuit that subserves this process.

Rheotaxis: This behavior, shared by most fish and amphibians, drives the animal to swim against an oncoming water flow. It is drivenby both the visual and lateral line system. We studied, from a behavioral view-point how these two sensory inputs contribute to the motor response. We now wish to identify the associated integrator centers and to dissect the neural circuit controling this multi-sensory process.

Chemical sensing: The question here is to understand how odors and tastants are coded in the brain. As a first step, we developed a microfluidic-based chip that enables delivering brief pulses of chemicals with 10ms time resolution, directly towards the face of apartially restrained larva. This device allows us to probe the effect of stimulus duration on the neuronal response along the sensorypathways.

Team members

Raphaël Candelier
Sergei Kruglik
Sébastien Wolf
Alexis Dubreuil
Sophia Karpenko
Guillaume Le Goc

Lab rotation

Sensorimotor computation underlying goal-directed locomotion in zebrafish

Team leader: 



January 2, 2018 - June 29, 2018

Application deadline: 

June 29, 2018


~ Jan-March 2018

~ April-June 2018


Using brain-wide functional imaging, in a virtual-reality setting, we aim to dissect the neural computation at play during goal-directed locomotion (such as phototaxis, thermotaxis, chemotaxis). We will in particular study how sensory cues may bias the statistics of spontaneous locomotory events (swim bouts) to  eventually drive the animal towards the most adequate regions of the environment. 


Laboratoire Jean Perrin - 4, place Jussieu 75005 Paris - +33 1 44 27 47 14 -